User: Aaron Mackey

gravatar for Aaron Mackey
Aaron Mackey200
Reputation:
200
Status:
Trusted
Location:
Last seen:
4 years, 9 months ago
Joined:
9 years, 10 months ago
Email:
a*******@gmail.com

Posts by Aaron Mackey

<prev • 21 results • page 1 of 3 • next >
0
votes
0
answers
880
views
0
answers
how to build a new crlmm CDF annotation package?
... I have Illumina "humanomni5exome-4v1-1_a" SNP chip idat files, but I don't believe I can/should use the existing "humanomni1quadv1bCrlmm" annotation package ... is there a way to build a custom CDF for it, given the annotation files available at: http://support.illumina.com/downloads/humanomni5exome ...
annotation crlmm written 4.8 years ago by Aaron Mackey200
0
votes
4
answers
1.6k
views
4
answers
Comment: C: limma, analysis on subset of data gives completely different results
... On Thu, Jul 17, 2014 at 11:21 AM, James W. MacDonald wrote: > On the other hand, you are increasing your degrees of freedom markedly by > including all the other groups, so your variance estimates will be much > more accurate (and you are then borrowing information from all groups to > ...
written 5.3 years ago by Aaron Mackey200
0
votes
1
answer
1.5k
views
1
answers
Comment: C: total count filter cutoff
... this is perhaps obvious to some, but I've seen colleagues surprised by it nonetheless: if each sample has been sequenced to a depth of ~20 million reads, then with cpm >= 1, you're effectively/approximately requiring raw counts >= 20; if your depth is 100 million reads, then you're requiring c ...
written 5.5 years ago by Aaron Mackey200
0
votes
1
answer
626
views
1
answers
Comment: C: edgeR
... My apologies -- I did not mean to sound confrontational, though I realize I probably did. Email is bad at that. I guess I was fishing for an expert's opinion on whether one of the two approaches is preferable (i.e. is one approach thought to be more powerful, better control of false positives, mor ...
written 5.5 years ago by Aaron Mackey200
0
votes
1
answer
626
views
1
answers
Comment: C: edgeR
... I'm surprised that the given answer here was to check whether two fold changes are themselves significant or not, rather than what I tend to think of as a "contrast of contrasts" scenario to test whether the two contrasts' fold changes are significantly different from another between groups (i.e. te ...
written 5.5 years ago by Aaron Mackey200
0
votes
2
answers
669
views
2
answers
Comment: C: Designing a model with blocking and other interactions
... Is this not a case for using duplicateCorrelation across the Family units, which would account for the correlation within a family, while still allowing for a mitoHap main effect? -Aaron On Thu, Apr 3, 2014 at 7:04 PM, Gordon K Smyth wrote: > On Thu, 3 Apr 2014, Eleanor Su wrote: > > ...
written 5.5 years ago by Aaron Mackey200
0
votes
0
answers
434
views
0
answers
B score-like posterior log-odds for edgeR topTags?
... I know topTags provides the LR test statistic; and I understand that a value of LR = 0 is a 50-50 chance of being a DEG. But is there a posterior log-odds transformation of the LRT (delta-deviance) value that can be interpreted the same way as limma's B score? My back of the envelop scribble seems ...
written 5.6 years ago by Aaron Mackey200
0
votes
1
answer
883
views
1
answers
Comment: C: Odd contrast; does it make statistical sense?
... As always, thanks Gordon for keeping the conversation focused. I guess I was responding to Ryan's statement that the only hypothesis to be tested was a difference between the two main groups, so the additional modeling of subgroups seems only to reduce the overall residual variance, possibly leading ...
written 5.7 years ago by Aaron Mackey200
0
votes
1
answer
883
views
1
answers
Comment: C: Odd contrast; does it make statistical sense?
... On Thu, Jan 23, 2014 at 6:48 PM, Gordon K Smyth wrote: > My worry is that with this contrast, I'm effectively just testing two >> groups against each other, and by having 4 groups in the design I will be >> estimating dispersions that are not appropriate for the test that I'm >&g ...
written 5.7 years ago by Aaron Mackey200
0
votes
2
answers
1.3k
views
2
answers
scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"
... A colleague of mine is skeptical of my assertion that drawing sample- level PCA plots and/or clustered heatmaps based only on differentially expressed genes (DEGs) is a circular, self-fulfilling prophecy -- they assert that there's no guarantee samples will cluster by condition (despite the fact tha ...
clustering written 5.9 years ago by Aaron Mackey200 • updated 5.9 years ago by Malcolm Cook1.5k

Latest awards to Aaron Mackey

Popular Question 4.8 years ago, created a question with more than 1,000 views. For scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 142 users visited in the last hour